When the Enterprise hovers above San Francisco looking for more whales, the Empire (who presumably based themselves there in honor of their creator) takes exception to the intruder, and hit it with everything they've got, from AT-ATs to VTOL TIE fighters and even the ultimate weapon, in orbit around the planet. The joke here is that in this reality's '80s, Reagan's "Star Wars" program was a LITERAL Star Wars program.

Note: if you had any issues whatsoever with the Enterprise being underwater in STID, you'll have a physics-related conniption here. But I think that'd be failing to see the space battle for the skyscrapers, y'know?